Data for "Cretaceous Chert‐Hosted Microfossils Visualized With Synchrotron Ptychographic X‐Ray Computed Tomography (PXCT)"

Supplemental data files and code for "Cretaceous Chert‐Hosted Microfossils Visualized With Synchrotron Ptychographic X‐Ray Computed Tomography (PXCT)," by Kelsey Moore, Theodore M. Present, Antoine Crémière, Manuel Guizar Sicairos, Mirko Holler, Andrew Barnett, Kristin Bergmann, Joachim Amthor, and John Grotzinger, published in Geobiology (2025), doi: 10.1111/gbi.70019.
Four PXCT datasets are archived here, corresponding to samples S4 and S8, each with two regions of interest (ROI), denoted S4_1, S4_2, S8_1, and S8_2. The PXCT data is in compressed ZIP archives.

"Sx_n slices.zip" archives include TIF files of scaled density data that are converted to electron densities using metadata in TXT files "Sx_n metadata.txt."
Cropped and scaled electron density data cubes are in multipage TIF files within "Sx_n_edensities.zip." (Note: electron densities in TIF volumes are in units of electrons per 10^4 cubic angstroms, e.g, 7123 as a pixel value is 0.7123 electrons per cubic angstrom. This is to permit storing electron densities as uint16 in the TIF volume with adequate precision.)
Several AVI files have movies of three-dimensional renderings of the PXCT data.
Matlab code for processing, fitting, and visualizing these data is in "PXCT_Code.zip." It was written in Matlab 2024b, and requires the Optimization Toolbox, Image Processing Toolbox, and Statistics and Machine Learning Toolbox. It is also available at https://github.com/presentt/PreSalt-PXCT
"GMmodels.zip" includes Matlab MAT files with the Gaussian Mixture model fit results and parameters, and two types of CSV files for the binned histogram data and the random subsample of each edensity dataset used for fitting.
Abstract
Silicification of microfossils is an important taphonomic process that provides a record of microbial life across a range of environments throughout Earth history. However, questions remain regarding the mechanism(s) by which silica precipitated and preserved delicate organic material and detailed cellular morphologies. Constraining the different mechanisms of silica precipitation and identifying the common factors that allow for microfossil preservation is the key to understanding ancient microbial communities and fossil‐preserving mechanisms. Here, we use synchrotron ptychographic X‐ray computed tomography (PXCT) as a novel technique to analyze microfossils from the Cretaceous Barra Velha Formation and better characterize their diverse morphologies and preservation styles. Through this technique, we generate 2D and 3D reconstructions that illustrate the microfossils and silica‐organic textures at nanometer resolution. At this resolution, we identify previously uncharacterized silica textures and organic‐silica relationships that help us relate findings from modern silicifying environments and experimental work to the fossil record. Additionally, we identify primary morphological differences among the microfossils as well as preservational variability that may have been driven by physiological and/or biochemical differences between the different organisms that inhabited the Cretaceous pre‐salt basin. These findings help us to better characterize the diversity and complexity of the microbiota in this ancient basin as well as taphonomic processes and biases that may have driven microfossil preservation in this and other silicifying environments throughout Earth history.
Keywords
Barra Velha Formation, chert, microfossil, pre-salt, ptychographic X‐ray computed tomography